Variant report

Variant	rs2609862
Chromosome Location	chr3:146259563-146259564
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:146257555-146263098	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:146257006-146262899	K562	blood:	n/a	n/a
3	POLR2A	chr3:146258807-146262913	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr3:146259543-146259814	MCF-7	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:146185173..146186845-chr3:146259254..146261120,2	K562	blood:
2	chr3:146234591..146236203-chr3:146259470..146262375,2	MCF-7	breast:
3	chr3:146254216..146256622-chr3:146257349..146260200,2	K562	blood:
4	chr3:146257059..146260785-chr3:146260976..146263871,3	MCF-7	breast:
5	chr3:146257750..146260238-chr3:146260636..146263970,4	K562	blood:

No data

Variant related genes	Relation type
PLSCR1	TF binding region
ENSG00000188313	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1057481	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1079369	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13064509	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13069082	0.86[ASN][1000 genomes]
rs1373246	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1443827	0.86[ASN][1000 genomes]
rs1882971	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882972	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882973	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882974	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1997601	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1997604	0.99[ASN][1000 genomes]
rs2120381	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2165948	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587007	0.99[ASN][1000 genomes]
rs2587008	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587009	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587010	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587011	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587012	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587013	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587014	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587015	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587016	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587017	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587018	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587021	0.84[EUR][1000 genomes]
rs2587023	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2587024	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609858	0.92[ASN][1000 genomes]
rs2609860	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609861	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609864	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609865	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609866	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609867	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2688688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738905	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738906	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738907	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738910	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2738911	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738912	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738915	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2738916	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738918	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738920	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2738923	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35214899	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35309521	0.80[ASN][1000 genomes]
rs3773510	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67703040	0.84[ASN][1000 genomes]
rs7615988	0.88[ASN][1000 genomes]
rs9289722	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs977758	0.86[ASN][1000 genomes]
rs9861142	0.88[ASN][1000 genomes]
rs9865918	0.88[ASN][1000 genomes]
rs9876886	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448053	chr3:146186791-146262066	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3523751	chr3:146186838-146261806	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv3523753	chr3:146186838-146261806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146225400-146260800	Weak transcription	NH-A	brain
2	chr3:146229000-146259600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr3:146231600-146260800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr3:146232000-146259600	Weak transcription	NHDF-Ad	bronchial
5	chr3:146233000-146259800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:146233000-146261400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr3:146247200-146260800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:146248800-146260800	Weak transcription	HSMM	muscle
9	chr3:146249000-146259600	Weak transcription	Aorta	Aorta
10	chr3:146249400-146260800	Weak transcription	NHLF	lung
11	chr3:146250600-146259600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr3:146250600-146260000	Weak transcription	Thymus	Thymus
13	chr3:146250600-146260800	Weak transcription	Fetal Kidney	kidney
14	chr3:146251600-146259600	Weak transcription	Colonic Mucosa	Colon
15	chr3:146252600-146259600	Weak transcription	Psoas Muscle	Psoas
16	chr3:146254600-146259600	Weak transcription	HMEC	breast
17	chr3:146254600-146261400	Weak transcription	Brain Germinal Matrix	brain
18	chr3:146254800-146259600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:146254800-146259800	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:146255000-146261000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:146255200-146259800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:146255200-146260800	Weak transcription	Placenta	Placenta
23	chr3:146255400-146260800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr3:146257000-146259800	Enhancers	Primary monocytes fromperipheralblood	blood
25	chr3:146257000-146260800	Enhancers	HepG2	liver
26	chr3:146257200-146261000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:146257200-146261000	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr3:146257200-146261200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr3:146257400-146259600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:146257400-146259600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:146257400-146259600	Weak transcription	Esophagus	oesophagus
32	chr3:146257400-146259600	Weak transcription	Gastric	stomach
33	chr3:146257400-146259600	Weak transcription	Pancreas	Pancrea
34	chr3:146257400-146259600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:146257400-146259800	Enhancers	Muscle Satellite Cultured Cells	--
36	chr3:146257400-146260800	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:146257400-146260800	Weak transcription	Lung	lung
38	chr3:146257400-146261200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:146257400-146261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:146257400-146261600	Weak transcription	Spleen	Spleen
41	chr3:146257400-146261800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:146257600-146259600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr3:146257600-146259600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:146257600-146259800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr3:146257600-146261400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
46	chr3:146257800-146259600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr3:146257800-146259600	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:146257800-146259600	Weak transcription	Left Ventricle	heart
49	chr3:146257800-146259600	Weak transcription	A549	lung
50	chr3:146257800-146260400	Enhancers	Primary T cells from cord blood	blood

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